15-91850865-T-C

Variant names:

• chr15-91850865-T-C
• rs7165398
• ENST00000761994.1:n.94+3221A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000761994.1(ENSG00000299260):​n.94+3221A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,100 control chromosomes in the GnomAD database, including 5,286 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.26 (5286 hom., cov: 32)
• Consequence: ENSG00000299260 ENST00000761994.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45
• Publications: 6 publications found

Genes affected

ENSG00000299260 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299260	ENST00000761994.1	n.94+3221A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38795 AN: 151980 Hom.: 5278 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.0183

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.260

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.255 AC: 38833 AN: 152100 Hom.: 5286 Cov.: 32 AF XY: 0.249 AC XY: 18504 AN XY: 74364

African (AFR) AF: 0.328 AC: 13594 AN: 41472

American (AMR) AF: 0.235 AC: 3592 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 965 AN: 3456

East Asian (EAS) AF: 0.0185 AC: 96 AN: 5176

South Asian (SAS) AF: 0.163 AC: 785 AN: 4826

European-Finnish (FIN) AF: 0.188 AC: 1988 AN: 10586

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16904 AN: 67982

Other (OTH) AF: 0.259 AC: 548 AN: 2116

Alfa AF: 0.247 Hom.: 17921

Bravo AF: 0.288

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.67
PhyloP100		-2.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7165398; hg19: chr15-92394095;